If you meet such an error :
C:\Program Files\MSBuild\Microsoft\WebDeployment\v8.0\Microsoft.WebDeployment.targets(474,9): error MSB6006: “aspnet_merge.exe” exited with code 1.
Go to VS 2005 > Tools> Options> Projects and solutions > Buid and run

and set dropdownlist value named : MSBuild project build output verbosity
In my case, I corrected my errors : problem with 2 differents aspx files named “default.aspx” and created by VS with “partial” attribute. This is a real problem because VS always use this syntax (partial class _Default) whereas the context (folder) are different and no namespace blocks are automatically generated.
So, after these correction, I obtain another error from aspnet_merge.exe : ” Index was outside the bounds of the array ” ????
…and no more information !
I tried all “merge” options (by page, by folder,…) and I always obtained this error whereas the basic compilation and execution works well.
An idea ?